[gmx-users] minimum image violation

[Kavyashree M]

Dear users,

    I ran 100ns simulation for 4 proteins, 3 of them were
non covalent dimers in solution, but only 1 is a covalent
dimer connected by a disulphide bridge. I used monomers
to run the job.
    Only in the case of covalent dimer I was getting severe
minimum image violation ie. out of 50001 data points,
282 are <= 1.4nm
280 are < 1.4nm
144 are < 1.3nm
79 are < 1.2nm
28 are < 1.1nm
4 < 1.0nm

I agree that this is quite wrong but I wanted to know whether
any useful information can be gathered out of this simulation?

In another data while calculating the energy terms it gives
nan (not a number error) for rmsd alone eg -
Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Temperature                     300      9e-05       -nan -0.000501989  (K)

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Pressure                    0.99914      0.027       -nan  0.0174391  (bar)

Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Volume                      517.755     0.0094       -nan   0.010871  (nm^3)

Initially i though some data points are missing but later
gmxcheck gives that all the data points are present.
now what could be the error?

I had asked this question before and was instructed to check the
trajectory. I checked the rmsd rmsf of this with the other proteins
it similar but one of the segment has high rmsf compared to the other
proteins.

Thanking you
With regards
M. Kavyashree
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